There has been an increasing concern about the effects of pathogens that are present in animal manure on humanand animal health. In recent years, outbreaks of food-borne diseases associated with the consumption of animal products havereceived much attention from the media in North America and Europe, leading to increased consumer concerns about the safety of their food supply. The health risks associated with animal operations depend on various factors. The most important ones appear to be related to the animal species being reared and the concentration of pathogenic microorganisms in animal manure. The ability of the pathogens to survive for long periods and through treatment to remain infective in the environment until ingested by human or animal host is an added concern. On the other hand, the role of livestock in most waterborne bacterial outbreaks has often been difficult to clarify since both humans and various wildlife species can shed the same microorganisms and thereby serve as sources of infection. This paper summarizes existing information on the main microbial pathogens present in livestock wastes, and discusses the impact of livestock wastes and agricultural drainage on microbiological quality of water, as well as available management and treatment technologies to minimize the prevalence of pathogens in animal wastes. Despite the fact that most disease outbreaks have been associated with food poisoning by cross-contamination during meat or milk processing and during finished product storage this review shows that a number of best management practices and technical solutions have been developed in the last few years that can be effective tools in minimizing the spread of pathogens from livestock operations in the environment.